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Table 2 Analysis of over- and under-represented MIPS annotations terms for differentially-expressed gene set

From: Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.)

MIPS FUNCTION number of elements on the array number of elements differentially expressed number of elements expected to be differentially expressed fold over or under represented p-value adjusted p-value
SUBCELLULAR LOCALIZATION 1263 3 50.25 -16.75 0 0
PROTEIN FATE (folding, modification, destination) 633 6 25.17 -4.20 9.11E-07 1.64E-05
PROTEIN SYNTHESIS 525 4 20.88 -5.22 1.18E-06 2.12E-05
CELLULAR COMMUNICATION/SIGNAL TRANSDUCTION MECHANISM 741 9 29.47 -3.27 2.26E-06 4.07E-05
ENERGY 439 3 17.48 -5.83 3.55E-06 6.38E-05
PROTEIN WITH BINDING FUNCTION OR COFACTOR REQUIREMENT (structural or catalytic) 618 7 24.58 -3.51 6.71E-06 1.21E-04
DEVELOPMENT (Systemic) 261 1 10.39 -10.39 2.67E-05 4.8E-04
CELL FATE 256 2 10.19 -5.09 3.79E-04 6.82E-04
INTERACTION WITH THE CELLULAR ENVIRONMENT 146 2 5.79 -2.90 0.02 0.37
BIOGENESIS OF CELLULAR COMPONENTS 542 12 21.58 -1.80 0.01 0.17
CELL CYCLE AND DNA PROCESSING 289 7 11.49 -1.64 0.06 1
TRANSCRIPTION 726 24 28.87 -1.20 0.17 1
CELL RESCUE, DEFENSE AND VIRULENCE 577 21 22.977 -1.09 0.33 1
CELLULAR TRANSPORT, TRANSPORT FACILITATION AND TRANSPORT ROUTES 758 28 30.17 -1.08 0.34 1
CLASSIFICATION NOT YET CLEAR-CUT 1072 44 42.66 1.03 0.59 1
UNCLASSIFIED PROTEINS 14494 711 565.43 1.26 1 1
METABOLISM 1737 111 69.13 1.61 1 1
STORAGE PROTEIN 30 4 1.20 3.34 0.97 1
  1. The number of differentially-expressed genes with a given MIPS annotation present on the array was used to determine the expected number of differentially-expressed genes with that annotation. The number of observed differentially expressed genes was compared to the expected number to provide a fold over or under representation. P-values and false discovery rates (adjusted P-values) were identified.